Protein stability thermodynamics

We present a molecular theory of hydration that now makes possible a unification of these diverse views of the role of water in protein stabilization. The central element in our development is the potential distribution theorem. We discuss both its physical basis and statistical thermodynamic framework with applications to protein solution thermodynamics and protein folding in mind. To this end, we also derive an extension of the potential distribution theorem, the quasi-chemical theory, and propose its implementation to the hydration of folded and unfolded proteins. Our perspective and current optimism are justified by the understanding we have gained from successful applications of the potential distribution theorem to the hydration of simple solutes. A few examples are given to illustrate this point. 

For a colloidal system containing a mixture of different biopolymers, in particular a protein-stabilized emulsion containing a hydrocolloid thickening agent, it is evident that the presence of thermodynamically unfavourable interactions (A u > 0) between the biopolymers, which increases their chemical potentials (thermodynamic activity) in the bulk aqueous phase, has important consequences also for colloidal structure and stability (Antipova and Semenova, 1997 Antipova et al., 1997 Dickinson and Semenova, 1992 Dickinson et al., 1998 Pavlovskaya et al., 1993 Tsap-kina et al., 1992 Semenova et al., 1999a Makri et al., 2005 Vega et al., 2005 Semenova, 2007). 

There seems to be a sort of analogy here with the arrested phase separation of a protein-stabilized depletion-flocculated emulsion containing a thermodynamically incompatible hydrocolloid like xanthan gum (Moschakis et al., 2005 Dickinson, 2006b). 

Thermodynamic and kinetic examination of protein stabilization by glycerol, Biochemistry 1981, 20, 4677 1686. 

Analysis of the dependence of the structural thermodynamics of globular proteins on apolar surface area provides an estimation of the role of various contributions to protein stability. However, as mentioned above, proteins also show convergence temperatures that can yield similar information, given certain assumptions. 

Fundamental Thermodynamic Parameters for Estimating Protein Stability from Crystal... 

It appears that the discreteness of a structure is a general principle of protein architecture, which not only reflects the evolution of the protein molecule but also has a deep physical ground (Privalov, 1985, 1986). It is just this unique thermodynamic property of the protein molecule that has made possible a quantitative definition of protein stability. 

Another common indication of protein stability is the concentration of either urea or GnHCl required to unfold half of the protein available. This concentration, given the symbol [D]i/2, is analogous to the Tm value from thermal denaturation curves. Increase or decrease in [D]i/2 is presumed to indicate a corresponding increase or decrease in protein stability, respectively. Analysis of these curves can also provide thermodynamic information [123-126]. As these experiments can be done at any temperature, they are more useful in that they can provide information regarding stability at or near room temperature. 

The thermodynamic description of protein stabilization, which involves the concept of preferential exclusion of stabilizing cosolvents, and the chemical description of osmophobicity of peptide linkages to stabilizing cosolvents represent two sides of a coin. The symmetry in these descriptions can perhaps best be appreciated by viewing osmophobicity as arising from the creation by a stabilizing cosolvent like TMAO of an aqueous phase whose structure is not favorable for hydration of the pep-... 

The entire thermodynamic system of the membrane and TM protein must be considered to understand how the protein and bilayer achieve their native state. We have summarized four of the mechanisms, hydrophobic matching, tilt angles, and specific protein/lipid and protein/protein interactions that are important in determining the stability (Fig. 5). Other important factors, such as the stability of lipid/lipid interactions, have been left out of our protein-centric view. We describe a hydrophobic mismatch as an unfavorable interaction that can be relieved by the other three processes, but we would expect all these properties of the system to interact. We could easily describe the same equilibria by saying that a strain in curvature is relieved by a hydrophobic mismatch or that strong protein/protein packing interactions might help relieve the hydrophobic mismatch or curvature stress. The complex interplay between all these interactions is at the heart of what determines membrane protein stability and will no doubt be difficult to quantify. 

Franks, F., Hatley, R. H. M and Friedman, H. L The thermodynamics of protein stability. Cold destabilization as a general phenomenon. Biophys. Chem. 31, 307-316 (1988). 

The applications of the chemistry of amino acids to the biological problem, protein structure and function, and folding and stability are the main focus of this article. The article is divided into hve main sections that include the biological insights on protein structures, chemical applications including protein functions, thermodynamics of proteins, protein interactions, and computational protein design. 

ProTherm (16) is a large collection of thermodynamic data on protein stability, which has information on 1) protein sequence and stmcture (2) mutation details (wild-type and mutant amino acid hydrophobic to polar, charged to hydrophobic, aliphatic to aromatic, etc.), 3) thermodynamic data obtained from thermal and chemical denaturation experiments (free energy change, transition temperature, enthalpy change, heat capacity change, etc.), 4) experimental methods and conditions (pH, temperature, buffer and ions, measurement and method, etc.), 5) functionality (enzyme activity, binding constants, etc.), and 6) literature. 

Consider next how this general ligand binding argument relates specifically to the Timasheff mechanism for solute-induced protein stabilization and destabilization. Detailed, rigorous reviews of the Timasheff mechanism can be found elsewhere (e.g., [78,79]). For the purpose of the current review a brief summary, which purposely provides only a simplified explanation, will suffice. First, a descriptive overview will be given, followed by an examination in more detail of the most relevant thermodynamic equations. 

In the past, we have ascribed these differences in protein stabilization to Timasheff s thermodynamic mechanism. The only protein for which the needed thermodynamic parameters have been measured in the presence of all three cryo-protectants is chymotrypsinogen [83,84] Table 1. Although these data are not directly applicable to LDH, the general trends shown should be relevant to any protein. The increase in chymotrypsinogen chemical potential, (6 i2/Sm3), in the presence of either of two different molecular weights of PEG (e.g., = 400 or... 

Mechanisms of Protein Stabilization During Freeze-Drying and Storage The Relative Importance of Thermodynamic Stabilization and Glassy State Relaxation Dynamics... 

Most protein stability studies have focused their interpretation on either a thermodynamic mechanism or a pure kinetic mechanism, and consequently there is some controversy and confusion over which mechanism is correct. Since the direction of a formulation development effort may depend on which theory is being followed, clarification of the roles of thermodynamic stabilization and kinetic stabilization in given stability problems would provide some practical benefit. This chapter is an attempt to provide such clarification. To this end, the major stresses, or destabilizing effects, that operate during the freeze-drying process are discussed, selected empirical observations regarding pharmaceutical stability in protein systems are presented, and the structure and dynamics in amorphous protein formulations are discussed. 

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